Swine Flu Intelligence Report

Swine flu: where do we stand?
It has been a little over two months since the first cases of infection by a new influenza strain were identified. What do we now know about this new flu strain? Here's an update from the World Health Organization that was released earlier this week:

As the A/H1N1 flu virus spreads further around the world, the World Health Organization (WHO) is getting closer to declaring a full pandemic, a senior official of the UN agency said on Tuesday, 6-2-2009.
"Globally we believe that we are at phase 5, but we are getting closer to phase 6," said WHO Assistant Director-general Dr. Keiji Fukuda, referring to the WHO's six-phase pandemic alert system.
The new virus is causing more and more infections in countries outside of North America, notably in Britain, Spain, Japan, Australia and Chile, Fukuda told a news conference in Geneva.
"We still are waiting for evidence of really widespread community activity in these countries," he said.
According to the WHO's current pandemic alert system, phase 6 will mean the A/H1N1 flu virus causes sustained and community-level human-to-human transmission in regions outside of North America, so far the only region where community-level outbreak has been confirmed.
So far the virus has caused nearly 19,000 cases of infections in 64 countries and regions, including 117 deaths, the WHO said.

Here is some background information on this new flu virus provided by the Centers For Disease Control and Prevention:

Novel influenza A (H1N1) is a new flu virus of swine origin that was first detected in April, 2009. The virus is infecting people and is spreading from person-to-person, sparking a growing outbreak of illness in the United States. An increasing number of cases are being reported internationally as well.
It's thought that novel influenza A (H1N1) flu spreads in the same way that regular seasonal influenza viruses spread; mainly through the coughs and sneezes of people who are sick with the virus. It's uncertain at this time how severe this novel H1N1 outbreak will be in terms of illness and death compared with other influenza viruses. Because this is a new virus, most people will not have immunity to it, and illness may be more severe and widespread as a result. In addition, currently there is no vaccine to protect against this novel H1N1 virus. CDC anticipates that there will be more cases, more hospitalizations and more deaths associated with this new virus in the coming days and weeks.

What are the real numbers?

In a recent New York Times article, writer Donald McGee contends that epidemiologists' computer simulations significantly underestimated the rate at which the new flu strain would spread. Here's a quote from the NYT article:

In the waning days of April, as federal officials were declaring a public health emergency and the world seemed gripped by swine flu panic, two rival supercomputer teams made projections about the epidemic that were surprisingly similar - and surprisingly reassuring. By the end of May, they said, there would be only 2,000 to 2,500 cases in the United States.
May's over. They were a bit off.
On May 15, the Centers for Disease Control and Prevention estimated that there were "upwards of 100,000" cases in the country, even though only 7,415 had been confirmed at that point.

In response to the NYT article, one government-funded epidemiologist replied:

"I think this is very poor journalistic performance. McNeil featured the predictions in the Times May 3, at which point decent data were almost impossible to come by and no one thought that these guys could have used real flu parameterizations to get their estimates. He should have been skeptical at the time. Now he is punishing them for their early hype, which it was his job to look into at the time, and at the same time making all of modeling look bad."

Now that we know the rates at which this new H1N1 strain is spreading, what does it mean?
First, the good news. While this new flu strain is spreading fairly rapidly, it is not as virulent as had been feared initially. As of the most recent CDC counts, there have been 13,217 laboratory confirmed cases of H1N1 in the United States, and 27 deaths attributed to the disease, representing an apparent mortality rate of approximately 0.2 percent. By comparison, compared with most other viral respiratory infections such as the common cold, normal seasonal influenza infection often causes a more severe illness with a mortality rate of about 0.1 percent of people who are infected with the virus.
Unusually severe worldwide outbreaks (pandemics) have occurred several times in the last 100 years since influenza virus was identified in 1933. By an examination of preserved tissue, the worst influenza pandemic occurred in 1918 when the virus caused between 40 to 100 million deaths with a mortality rate estimated to range from 2 percent to 20 percent.

Speaking of the 1918 pandemic...
There are a few interesting similarities between the current swine flue outbreak and the one which occurred in 1918. First, they are both H1N1 flu strains. Second, the initial outbreak in each case occurred in the northern hemisphere, in the spring. In 1918 the initial outbreak was of a relatively mild strain, as has been the case for the current outbreak. However, in the fall of 1918, which is when the normal "flu season" starts, a mutated and much more virulent form of the virus re-emerged, and it was this mutated virus that led to the large number of deaths. This fact has not been lost on epidemiologists who are studying the current outbreak and who will be carefully watching for signs of the emergence of a new mutated strain.

What's different between 1918 and today?
Health officials have studied the 1918 pandemic, and subsequent outbreaks which occurred in 1957 and 1968 and as a result have learned much about the patterns of influenza outbreak, and about what kinds of intervention strategies can be effective in slowing the spread of the disease. Today we have antiviral medications, and the ability to produce vaccines for use against new strains of influenza.
The CDC and the U.S. Food and Drug Administration have created a candidate vaccine virus for swine flu, also known as 2009 H1N1, using reverse genetics. Vaccine makers will tweak the virus and have "pilot lots" of vaccine ready to be tested by mid- to late June.

What to do in the mean time
On May 22, the CDC published this advice on their web site:
In areas with confirmed human cases of novel influenza A (H1N1) virus infection, the risk for infection can be reduced through a combination of actions. No single action will provide complete protection, but an approach combining the following steps can help decrease the likelihood of transmission. These recommended actions are:

Wash hands frequently with soap and water or use alcohol-based hand cleaner when soap and water are not available.

Cover your mouth and nose with a tissue when coughing or sneezing.

Avoid touching your eyes, nose and mouth

People who are sick with an influenza-like illness (ILI) (fever plus at least cough or sore throat and possibly other symptoms like runny nose, body aches, headaches, chills, fatigue, vomiting and diarrhea) should stay home and minimize contact with others, including avoiding travel, for 7 days after their symptoms begin or until they have been symptom-free for 24 hours, whichever is longer.

Avoid close contact (i.e. being within about 6 feet) with persons with ILI.

Doug Roberts worked at Los Alamos National Laboratory for 20 years, during which time he and his team developed a large-scale epidemiological simulation named EpiSims. EpiSims is still in use, and is currently running on several high performance compute clusters at various locations in the US. Doug presently telecommutes to work for a company in the Research Triangle Park in North Carolina.